diff --git a/apps/server/src/vcs/GitVcsDriver.test.ts b/apps/server/src/vcs/GitVcsDriver.test.ts
index fd85564a7dadd..4d442d7194a91 100644
--- a/apps/server/src/vcs/GitVcsDriver.test.ts
+++ b/apps/server/src/vcs/GitVcsDriver.test.ts
@@ -193,6 +193,7 @@ it.effect("checkpoint capture skips untracked nested repositories without a comm
       `160000 commit ${nestedHead}\tcommitted\n`,
     );
     assert.deepEqual(yield* fileSystem.readFile(path.join(cwd, ".git", "index")), originalIndex);
+    assert.isTrue(yield* driver.checkpoints.restoreCheckpoint({ cwd, checkpointRef }));
     assert.strictEqual(
       yield* fileSystem.readFileString(path.join(cwd, nested, "private.txt")),
       "nested\n",
@@ -1113,6 +1114,8 @@ it.effect("restores empty checkpoints without changing paths outside the workspa
       yield* fileSystem.writeFileString(path.join(cwd, "ignored.txt"), "keep\n");
       yield* fileSystem.makeDirectory(path.join(cwd, "untracked"));
       yield* fileSystem.writeFileString(path.join(cwd, "untracked", "file.txt"), "remove\n");
+      yield* fileSystem.writeFileString(path.join(cwd, "untracked", ".gitignore"), "hidden.txt\n");
+      yield* fileSystem.writeFileString(path.join(cwd, "untracked", "hidden.txt"), "remove\n");
       assert.isTrue(
         yield* driver.checkpoints.restoreCheckpoint({ cwd, checkpointRef, fallbackToHead: false }),
       );
@@ -1130,6 +1133,43 @@ it.effect("restores empty checkpoints without changing paths outside the workspa
         });
         assert.strictEqual(staged.stdout.trim(), "outside.txt");
       }
+      yield* fileSystem.writeFileString(path.join(cwd, "checkpoint.txt"), "checkpoint\n");
+      yield* driver.checkpoints.captureCheckpoint({ cwd, checkpointRef });
+      yield* fileSystem.writeFileString(path.join(cwd, "checkpoint.txt"), "later\n");
+      let deepest = cwd;
+      for (let depth = 0; depth < 4; depth++) {
+        yield* fileSystem.writeFileString(path.join(deepest, ".gitignore"), "d/.gitignore\n");
+        deepest = path.join(deepest, "d");
+        yield* fileSystem.makeDirectory(deepest);
+      }
+      yield* fileSystem.writeFileString(path.join(deepest, ".gitignore"), "hidden.txt\n");
+      yield* fileSystem.writeFileString(path.join(deepest, "hidden.txt"), "remove\n");
+      const incomplete = yield* driver.checkpoints
+        .restoreCheckpoint({ cwd, checkpointRef, fallbackToHead: false })
+        .pipe(Effect.flip);
+      assert.strictEqual(incomplete._tag, "VcsProcessExitError");
+      assert.strictEqual(
+        yield* fileSystem.readFileString(path.join(cwd, "checkpoint.txt")),
+        "checkpoint\n",
+      );
+      assert.strictEqual(
+        (yield* driver.execute({
+          operation: "test",
+          cwd,
+          args: ["diff", "--cached", "--name-only", "--", "."],
+        })).stdout,
+        "",
+      );
+      if (nested) {
+        assert.strictEqual(
+          (yield* driver.execute({
+            operation: "test",
+            cwd: root,
+            args: ["diff", "--cached", "--name-only"],
+          })).stdout.trim(),
+          "outside.txt",
+        );
+      }
     }
   }).pipe(Effect.scoped, Effect.provide(layerGitContract)),
 );
diff --git a/apps/server/src/vcs/GitVcsDriver.ts b/apps/server/src/vcs/GitVcsDriver.ts
index d3ecfcfa95d73..569eda70cd7d8 100644
--- a/apps/server/src/vcs/GitVcsDriver.ts
+++ b/apps/server/src/vcs/GitVcsDriver.ts
@@ -1339,13 +1339,52 @@ export const makeVcsDriverShape = Effect.fn("makeGitVcsDriverShape")(function* (
             }),
         ),
       );
+      const resetIndex = Effect.gen(function* () {
+        // On Windows clean can remove './' and exit 0.
+        yield* recreateWorkspace;
+        yield* execute({
+          operation,
+          cwd: input.cwd,
+          args: [...longPaths, "reset", "--quiet", "--", "."],
+        });
+      });
       yield* recreateWorkspace;
-      const cleaned = yield* execute({
+      const clean = execute({
         operation,
         cwd: input.cwd,
         args: [...longPaths, "clean", "-fd", "--", "."],
+        env: { LC_ALL: "C" },
         allowNonZeroExit: true,
       });
+      let cleaned = yield* clean;
+      // Removing a new .gitignore exposes the files it hid; clean again until nothing is left.
+      for (
+        let pass = 1;
+        pass < 4 && cleaned.exitCode === 0 && /^Removing /m.test(cleaned.stdout);
+        pass++
+      ) {
+        yield* recreateWorkspace;
+        cleaned = yield* clean;
+      }
+      if (cleaned.exitCode === 0 && /^Removing /m.test(cleaned.stdout)) {
+        yield* recreateWorkspace;
+        const remaining = yield* execute({
+          operation,
+          cwd: input.cwd,
+          args: [...longPaths, "clean", "-dn", "--", "."],
+          env: { LC_ALL: "C" },
+        });
+        if (/^Would remove /m.test(remaining.stdout)) {
+          yield* resetIndex;
+          return yield* new VcsProcessExitError({
+            operation,
+            command: "git clean",
+            cwd: input.cwd,
+            exitCode: 0,
+            detail: "Could not clean the checkpoint workspace: untracked files remain.",
+          });
+        }
+      }
       if (cleaned.exitCode !== 0) {
         // Git can remove every child, then fail trying to remove './' itself.
         const emptiedWorkspace =
@@ -1355,7 +1394,8 @@ export const makeVcsDriverShape = Effect.fn("makeGitVcsDriverShape")(function* (
             Effect.map((entries) => entries.length === 0),
             Effect.orElseSucceed(() => false),
           ));
-        if (!emptiedWorkspace)
+        if (!emptiedWorkspace) {
+          yield* resetIndex;
           return yield* new VcsProcessExitError({
             operation,
             command: "git clean",
@@ -1363,15 +1403,9 @@ export const makeVcsDriverShape = Effect.fn("makeGitVcsDriverShape")(function* (
             exitCode: cleaned.exitCode,
             detail: cleaned.stderr.trim() || "Could not clean the checkpoint workspace.",
           });
+        }
       }
-      // On Windows the same clean can remove './' and exit 0.
-      yield* recreateWorkspace;
-
-      yield* execute({
-        operation,
-        cwd: input.cwd,
-        args: [...longPaths, "reset", "--quiet", "--", "."],
-      });
+      yield* resetIndex;
 
       return true;
     }),